|I can't use for instance cron, because the sheduling is done in a different system.
You lost me. Why can't you use cron? You can put a CGI or GUI frontend on it if you want, and have it write edits out to crontab (there's a module for that).
Also if i just execute the perl programms through the sheduling system, i have a scalabilty problem ... like the cgi problem with httpd, addressed with mod_perl.
mod_perl doesn't reduce concurrency. It elminates the need to fork at request time (by forking ahead of time) and allows persistent connections to databases. Both of those help performance a lot. If you think that would help your situation, you could try re-writing your programs as mod_perl modules, and calling them from cron via LWP.
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